Dear Ross,
I tried the same procedure with leaprc.ff99 but I still had the same
problem. The system I am modelling is a monofunctional Pt complex bound
to a guanine, the chlorine is coordinated to the platinum. According to
your tutorial I guess I should edit the guanine residue in DNA and
create a new one with the complex on it. I will try this procedure and
I'll keep you posted.
Many Thanks.
Atilio.
> Dear Atilio,
>
>> I am trying to bind a metal complex to a small DNA seqence
>> in xleap, I
>> loaded the metal complex as a prepin file and created the Pt-N bond
>> with DNA. But when trying to save parameters and input coordinates I
>> got the following message:
>>
>> For atom: .R <<1> 35> .A <Cl 1> could not find type:Cl
>> Parameter file was not saved.
>
> See this tutorial->
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm
>
>
> This will show you how to add Pt atom types and add the parameters for the
> Pt-N bond. As for the error about unfound atom type Cl what force field
> file
> did you load when you ran leap? Do you have a stray chlorine atom in your
> pdb file or was this chlorine added by an addions command?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 |
> | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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Received on Thu Mar 17 2005 - 16:53:01 PST
